!tr ',' "\t" </Volumes/web/scaphapoda/Grace/Olur_goslim_a.csv> /Volumes/web/scaphapoda/Grace/Olur_goslim_a.tab
-out /Volumes/web/scaphapoda/Grace/olur_goslim_uniprot.tab
--------------------------------------------------------------------------- NameError Traceback (most recent call last) <ipython-input-5-9f20d9d76b3c> in <module>() 1 get_ipython().system(u'tr \',\' "\\t" </Volumes/web/scaphapoda/Grace/Olur_goslim_a.csv> /Volumes/web/scaphapoda/Grace/Olur_goslim_a.tab') ----> 2 -out /Volumes/web/scaphapoda/Grace/olur_goslim_uniprot.tab NameError: name 'out' is not defined
!head /Volumes/web/scaphapoda/Grace/Olur_goslim_a.tab
!tail /Volumes/web/scaphapoda/Grace/Olur_goslim_a.tab
!fgrep --color "gonad" /Volumes/web/scaphapoda/Grace/Olur_goslim_a.tab
!wc -l /Volumes/web/scaphapoda/Grace/Olur_goslim_a.tab
5907 /Volumes/web/scaphapoda/Grace/Olur_goslim_a.tab
#make a pie chart
figure(1, figsize=(6,6))
ax = axes([0.1,0.1,0.8,0.8])
labels = 'Reproduction', 'Growth', '
--------------------------------------------------------------------------- NameError Traceback (most recent call last) <ipython-input-10-82537392d5d3> in <module>() ----> 1 figure(1, figsize=(6,6)) 2 ax = axes([0.1,0.1,0.8,0.8]) NameError: name 'figure' is not defined
!head /Volumes/web/scaphapoda/Grace/Olur_goslim_a.tab
!awk '{print $4}' /Volumes/web/scaphapoda/Grace/Olur_goslim_a.tab | sort | uniq
14332_CAEEL 1433E_DROME 1433G_BOVIN 2AAA_PIG 3HAO_BURCJ 41_DROME 4EBP1_HUMAN 6PGL1_ARATH AATM_CHICK AATR3_SCHPO AB5C_ARATH ABAMS_PEA ABCA3_DICDI ABL1_CAEEL ACADM_MOUSE ACD11_RAT ACH1_MANSE ACHA2_MOUSE ACHA7_CHICK ACL6B_RAT ACON_MOUSE ACOX1_RAT ACOX3_HUMAN ACPH_RAT ACPM_BOVIN ACPS_STAES ACSA_DROME ACTN_DROME ADA10_RAT ADGB_MOUSE ADK2_ARATH ADOK_MYCTU ADO_RABIT ADRM1_XENTR ADT_CHLRE AGO7_ORYSJ AGRB_STACT AIF1_HUMAN AIFM1_DICDI AJSP1_TRINI AKD1_HUMAN AKP13_HUMAN AKTP1_DROVI AL1B1_PONAB ALA5_ARATH ALG5_DICDI ALKN_ALCBS ALX4_BOVIN AMOT_HUMAN AMY_PECMA ANGL7_HUMAN ANK2_HUMAN ANPRA_HUMAN ANPRA_MOUSE ANR42_MOUSE ANR54_BOVIN ANRA2_HUMAN ANXA6_BOVIN ANXA7_BOVIN AP2A_MOUSE AP3B_YEAST AP4S1_MOUSE APBLB_ARATH APBP2_RAT APC10_HUMAN APKT1_ANTEL APLP_LOCMI APOD_HUMAN APY_BIFBA ARC1A_HUMAN ARF2_RAT ARG13_NEUCR ARGC_DICTD ARGC_SHEWM ARHG6_CHICK ARHGC_HUMAN ARID2_HUMAN ARSE_MACFA ASAP1_HUMAN ASM_MOUSE ASO_CUCSA ASPP1_MOUSE AT1A_TAESO AT5F1_HUMAN AT5G_MANSE ATC1_DICDI ATE_BRUMB ATE_VIBCM ATG1_PICAN ATG7_CHICK ATGA1_XENTR ATM_NEUCR ATOH8_MOUSE ATP5E_BOVIN ATP5H_MOUSE ATPA_PONAB ATPB_DROME ATPG_AKKM8 ATPG_DROME ATPO_DROME ATRIP_MOUSE AURAB_XENLA AUTS2_HUMAN B2CL1_HUMAN B2MG_PIG B3GN5_XENTR BACA_MYCTU BACD3_MOUSE BAMBI_RAT BASS2_ARATH BC11B_MOUSE BCORL_MOUSE BETI_BURTA BGAL_PSYIN BGBP_PENMO BIRC6_HUMAN BT3L4_DANRE BTG1_CHICK BZW1_CHICK C1QBP_RAT C3H64_ARATH CA095_MOUSE CAAT1_ARATH CAD12_HUMAN CAD23_MOUSE CAH8_MOUSE CALR_RABIT CAN10_HUMAN CAN7_MOUSE CANB1_RAT CAPZA_DROME CASP7_MESAU CATA_PONAB CATB_PIG CATL1_CANFA CATL2_HUMAN CATL_SARPE CATL_SCHMA CATR_TETST CAV1_ATEAB CBPA1_ANOGA CBPB_ASTAS CBP_MOUSE CBR1_HUMAN CBRA_DICD3 CBX3_MOUSE CC113_MOUSE CC162_MOUSE CCD15_MOUSE CCD39_XENTR CCD96_MOUSE CCGL_HUMAN CCNI_MOUSE CCNL1_XENLA CCR6_MOUSE CCS1_CYACA CD63_MOUSE CD9_RAT CDC27_HUMAN CDC42_ASHGO CDD_PASMU CDKL1_HUMAN CDKL2_PONAB CDYL2_HUMAN CEBPD_RAT CEBPG_HUMAN CENPB_CRIGR CENPJ_MOUSE CHD4_HUMAN CHD9_HUMAN CHERP_MOUSE CHIT1_HUMAN CHIT3_DROME CHKB_RAT CHLB_SYNP2 CHLN_CHLRE CHP2_RAT CHSS2_CAEEL CITC_ECOLI CKLF4_HUMAN CLC2F_MOUSE CLU_SCHPO CNO6L_MOUSE CO4A1_CAEEL CO6A5_HUMAN COFI_ZYGRO COG6_CAEEL COMD5_HUMAN COTL1_BOVIN COX12_SCHPO COX1_ALBTU COX1_OSTNU COX2_BRALA COX3_ALBCO COX3_LOCMI COX42_THUOB COX5B_HUMAN CP110_HUMAN CP1A1_CANFA CP3AD_MOUSE CP4AO_PIG CP4F3_RAT CP91_CONRE CPVL_PONAB CRIP1_HUMAN CROCC_HUMAN CROM_ENTDO CRYL1_PONAB CSAD_HUMAN CSDE1_HUMAN CSP1_ARATH CSPP1_HUMAN CTBL1_BOVIN CTL2_XENLA CTNA_DICDI CTND1_HUMAN CTNS_BOVIN CUBN_CANFA CUL3B_XENLA CUL4A_HUMAN CXE8_ARATH CY1_BOVIN CYAA_SCHPO CYB_CHABA CYB_KRYMA CYB_OCHAL CYC5_PSEME CYC_PECGU CYGB1_ORYLA CYGB2_DANRE CYHR1_BOVIN CYP6_CAEEL CYSP1_DICDI CYTB_RAT Column4 DAD1_RAT DAPA_ERYLH DAPB_ASPTN DAPB_DESAD DCC_HUMAN DCDA_ORYSJ DCOR_CHICK DCUP_HUMAN DDL_LISMF DDX42_CHICK DED1_DEBHA DEGPL_BARHE DELE_RAT DEP1A_HUMAN DFNA5_MOUSE DHE3_HUMAN DHRS1_MOUSE DHSAB_XENLA DHSB_XENLA DIRC2_XENLA DJB12_MOUSE DMBT1_HUMAN DNLJ_PSYIN DOPO_RAT DP2L_PICTO DPB2_YARLI DPGN_DIPMA DPH1_CANAL DPH5_MOUSE DPHS1_ARATH DQA1_HUMAN DRG2_HUMAN DSCL1_HUMAN DSCL_DROME DTBP1_HUMAN DUS4_RAT DUS7_MOUSE DX39B_DROME DXS_AZOPC DYH10_HUMAN DYH1_HUMAN DYH2_HUMAN DYH3_HUMAN DYH5_HUMAN DYH5_MOUSE DYH6_HUMAN DYH7_HUMAN DYH7_RAT DYHC2_PLAF7 DYHC_EMENI DYHC_TRIGR DYL2_RAT DYRK4_MOUSE E74EB_DROME EAPP_MOUSE EAT20_CAEEL EBP_MOUSE ECHA_HUMAN EF1A_APIME EF1A_DANRE EF1G2_YEAST EF1G_RABIT EF2_CAEEL EFC4B_HUMAN EFCB5_MOUSE EFCB6_HUMAN EFHC2_DANRE EFTS_CROS8 EGTB_MYCTU EHF_BOVIN EI2BE_MOUSE EIF2A_CHICK EIF3E_RAT EIF3G_DANRE EIF3H_RAT ELF3_MOUSE ELF5_HUMAN ELO3_CAEEL ELOB_RAT ELOC_RAT EMAL1_MOUSE ENOPH_BRAFL ENO_DORPE ENO_PORGI ENTK_PIG ENTP2_HUMAN EP400_HUMAN EPDR1_HUMAN EPDR1_MACFA EPG5_AEDAE ERCC5_XENLA ERG_CHICK ERI1_MOUSE ES1_MOUSE ESTD_RAT EXD1_MOUSE EXOC4_RAT EXOS7_HUMAN F186A_MOUSE F219B_MOUSE F264_RAT FA65B_MOUSE FA8_CANFA FAAA_BOVIN FABA_BAUCH FABP4_BOVIN FABP4_PIG FABP7_CHICK FACR1_MOUSE FAD5A_DICDI FAIM1_BOVIN FAS_CHICK FAT4_MOUSE FBN2_MOUSE FBRL_XENLA FBXW7_HUMAN FGF19_HUMAN FKB1A_XENLA FLNA_DROME FLNB_HUMAN FLOT1_DROME FLRT1_HUMAN FLUG_EMENI FMO5_MOUSE FOXK2_XENLA FREM1_HUMAN FREM2_HUMAN FRIH_TREBE FRIS_LYMST FRIY_LYMST FRM4A_MOUSE FTHS_THEM4 FTM_HUMAN FUBP2_MOUSE FUBP3_HUMAN FUSD_BURCE FZD5_XENLA FZD7_MOUSE FZR_MOUSE G3P_PANVR GABT_HUMAN GADL1_XENTR GAG_HTLV2 GBB_PINFU GBG12_BOVIN GBG7_HUMAN GBLP_ORENI GBRAP_RAT GBRL2_RAT GCDH_HUMAN GCH1_CHICK GCSPB_CHLPD GELS2_LUMTE GEMI2_XENLA GGT1_RAT GLB_NASMU GLCE_HUMAN GLGB_CHLFF GLMU_COXBU GLMU_ZYMMO GLYA_RUTMC GLYC_SHEEP GMPR1_HUMAN GNAO_MIZYE GOGB1_HUMAN GOLP3_HUMAN GORS2_MOUSE GP158_MOUSE GPBL1_MOUSE GPMI_VIBF1 GPPA_VIBFM GPTC8_HUMAN GPX1_SCHMA GPX5_RAT GRDN_MOUSE GRLN_DICDI GSCR2_HUMAN GSH1_ERWCT GSK3B_MOUSE GSTO1_RAT GT2D2_MOUSE GTR1_BOVIN H1_LYTPI H2AV_STRPU H33_XENTR H90A1_DANRE HCN2_RAT HDC_DROME HDHD2_PONAB HEBP2_MOUSE HELB_HUMAN HEM2_PEA HEMH_XENLA HEPF1_PLAF7 HES4_XENTR HEXI1_RAT HINT1_RABIT HISX2_PELUB HISX_DECAR HKDC1_MOUSE HLF_MOUSE HLF_RAT HLYD_PASSP HMCN1_HUMAN HMG2_DROME HMR1_CAEEL HNF6_MOUSE HNRPD_HUMAN HNRPQ_HUMAN HNRPR_HUMAN HPDL_HUMAN HPGDS_CHICK HPPD_RAT HS12B_MOUSE HSBP1_HUMAN HSDL2_DANRE HSP31_YEAST HSP7C_RAT HTAI2_HUMAN HTS_DROME HUTI_ROSDO HVCN1_CHICK HXK2_DROME HYCCI_HUMAN HYD_DROME I23O_YEAST ID2_XENTR IDHP_BOVIN IF2G_CHICK IF43B_SALSA IF4A2_RAT IF4E_APLCA IF4G2_RABIT IF5A1_RABIT IF6_MOUSE IFT20_DANRE IFT74_MOUSE IFT80_MOUSE IGO2_YEAST IKBA_PIG ILVD_SHESR IMPL2_DROME INT1_MOUSE INTU_XENLA IOVO_DRONO IPNS_PENCH IQEC1_HUMAN IRF2_SIGHI ISPG_CHLAB ITBX_DROME JIP4_MOUSE JKAMP_HUMAN JUN_SERCA KAD6_PYRAE KAD7_HUMAN KAE1_SCHPO KALRN_RAT KANK1_HUMAN KAPC_DROME KAPR_ASPFU KARG_LIOJA KAZD1_MOUSE KBX3_PANIM KCNH2_MOUSE KCNQ5_HUMAN KCP_XENLA KDUI_KINRD KEX1_PHANO KGUA_MOUSE KGUA_MYCPE KIF3A_HUMAN KIF3A_MOUSE KIF9_MOUSE KLC_CAEEL KLF5_HUMAN KLHL5_HUMAN KMO_LEGPL KMT2B_MOUSE KPSH1_PINFU KTAP2_IXOSC KTNB1_HUMAN KY_MOUSE LANC3_DROME LAP4A_CHICK LDLR_HUMAN LEG7_HUMAN LEP_PHOVI LEU3_AZOVI LEUC2_RUBXD LIAS_HUMAN LIN2_LOTJA LIPA_BACCN LIPA_OLICO LITAF_CHICK LITAF_HUMAN LON_AQUAE LON_ELUMP LPH_HUMAN LPP3_HUMAN LRC4B_MOUSE LRGUK_MOUSE LSM6_MOUSE LYST_BOVIN LYS_CRAGI L_WWAVU M22_AMPV1 M28P1_AJECN M2GD_HUMAN M3K4_MOUSE MACF1_RAT MAF_CHICK MARE1_XENTR MATK_BARLO MATN2_HUMAN MAX_HUMAN MBL1_RAT MCCA_HUMAN MCM4_DROME MCMBP_XENTR MCPI_MELCP MDH1B_BRAFL MDHC_CHICK MEC2_CAEEL MED15_DANRE MED19_AEDAE MED25_XENLA MEF2C_PIG MELT_DANRE MEP1A_MOUSE MEP1B_HUMAN META_BREBN METH_BOVIN MFGM_HUMAN MFHA1_XENTR MGST1_HUMAN MHPC2_PSEPU MIAA_LACAC MIAB_THELT MICAL_DROME MIEAP_DANRE MIEN1_MOUSE MIF_SHEEP MITF_MOUSE MKNK1_XENTR MLXIP_HUMAN MNMA_CHLFF MNMG_NOVAD MOAB_PYRFU MOT12_XENTR MOT5_HUMAN MP2K6_HUMAN MPCP_MOUSE MPPB_HUMAN MRAY_STRP4 MRC1_MOUSE MRC2_MOUSE MRGRD_HUMAN MSB1A_DANRE MSC1_SCHPO MSH3_MOUSE MSRB3_PONAB MTLD_STRR6 MTND_BRAFL MTX1_MACFA MUC1_HUMAN MURC_DESAH MUTL_DICNV MUTS_PROM9 MUTS_RICTY MYBPP_RAT MYLK3_DANRE MYLK_CHICK MYOF_MOUSE MYOM2_APLCA MYPH_ECHGR MYSA_DROME NAC3_RAT NACA_ORENI NAMPT_PIG NARE_CHICK NAS10_CAEEL NAT6_MOUSE NBR1_MOUSE NCAN_MOUSE NCAP_I63A2 NCOA5_MOUSE NCPR_MUSDO NDKB_MOUSE NDUA9_RAT NDUAA_DROME NDUB3_MOUSE NDUB5_PANTR NDUBB_BOVIN NDUV1_PONPY NDVB_RHIME NEC2_PONAB NETR_SAGLB NF2L1_CHICK NHRF1_RABIT NK3R_CAVPO NKX62_HUMAN NLRC3_HUMAN NNTM_BOVIN NORW_ERWCT NOS3_MOUSE NPC1_MOUSE NPC2_DROME NPC2_PANTR NPHN_RAT NPL_MOUSE NRDJ_BRAJA NRF6_CAEEL NRG_DROME NSMA_RAT NSPS_VIBCH NTE1_PHANO NTPA_HYDS0 NTRK2_MOUSE NU1M_ALBCO NU4M_LUMTE NU5M_DROME NU6M_ONCMY NUA4L_MOUSE NUC1_CAEEL NUCL_MOUSE NUF2_EMENI NUOH_MAGSM NUP54_RAT NUPR1_RAT OAT_DROAN OAZ1_DANRE OCCT_RHIRD ODBB_BOVIN ODP2_MOUSE OLA1_DROME ORC5_DICDI P2RX1_HUMAN P85A_BOVIN PA2G3_HUMAN PAAK_AZOEV PABP1_MOUSE PAFA_CANFA PAIN_DROME PAIRB_MOUSE PAK1_HUMAN PANC_DESMR PAPSS_URECA PARG_BOVIN PARPT_HUMAN PCBP3_HUMAN PCD18_MOUSE PCDB7_HUMAN PCDH8_HUMAN PCFT_DANRE PCGF3_HUMAN PCKA_WIGBR PCKGC_CHICK PCP1_SCHPO PDC10_XENLA PDCD4_CHICK PDE1B_MOUSE PDE6_DROVI PDIA1_HUMAN PDIA3_CHICK PDIP3_MOUSE PDK4_HUMAN PDLI1_MOUSE PE1_ANOGA PE48_CHRBE PECR_HUMAN PEF1_HUMAN PEPL1_MOUSE PEX10_HUMAN PFD1_DANRE PFD4_HUMAN PFD5_HUMAN PGDH_MOUSE PICK1_RAT PIN4_DANRE PINK1_MOUSE PIWL1_MOUSE PKD2_CAEEL PKHL1_MOUSE PKND_PARUW PKS30_DICDI PLAS_PEA PLB1_HUMAN PLB1_MONDO PLIN2_HUMAN PLK3_HUMAN PLPL2_HUMAN PLSX_LACCB PMA7_ARATH PME54_ARATH PML_MOUSE PNCB_BRAJA PNKP_HUMAN PNO1_DANRE POLG_CXB3W POL_COYMV POL_SIVMK PP168_ARATH PP1A_RAT PP1B_RAT PP2AB_RAT PP2B3_DROME PP4R1_HUMAN PPAL_BOVIN PPCEL_CHICK PPIA_BLAGE PPIA_STRAQ PPIB_CHICK PPIL6_HUMAN PPIP1_HUMAN PPM1B_MOUSE PPP6_HUMAN PPT1_MACFA PRDX5_HUMAN PRDX6_BOVIN PRIA_RICFE PRIB_SHEHH PROF2_ACACA PROF_ENTHI PRP4B_DICDI PRP8_MOUSE PRSS8_HUMAN PRTG_CHICK PSA4_HUMAN PSA6_RAT PSBH_WHEAT PSBP_PORPU PSD10_RAT PTBP1_RAT PTN1_CHICK PTRD1_BOVIN PUP16_ARATH PUR1_RAT PUR6_CHICK PURA_MOUSE PVR_HUMAN PXDN_HUMAN PYGM_MOUSE PYR1_HUMAN PYRB_FINM2 PYRB_STRTD PZRN3_RAT QCR2_HUMAN QCR7_FASHE QCR9_KLULA QKIB_XENLA QOR_HUMAN R10AB_DROME R1A6_SOLDE RAB5C_CANFA RAB6B_MOUSE RAB7A_BOVIN RABL_MIMIV RAC1_RAT RADI_MOUSE RAN_BRUMA RARGA_DANRE RBFA_VEREI RBGP1_MOUSE RBM10_HUMAN RBM14_MOUSE RBM39_PONAB RBOHJ_ARATH RBP2_MOUSE RBSD_ECOSE RBX1_SALSA RDH11_HUMAN RDRP_BAVJK RECO_HAMD5 RENT1_MOUSE RENT2_ARATH RESTB_XENLA RFCL_THEPD RFOX3_HUMAN RGA4_SCHPO RGMA_CHICK RGN_DANRE RGS22_HUMAN RGYR_PYRKO RHBGB_XENLA RHO_APLCA RK18_GRATL RL10_DROME RL11_RAT RL12_HUMAN RL13A_BOVIN RL13_DANRE RL14_LUMRU RL15_CYPCA RL17_ARGMO RL18A_HUMAN RL18_RAT RL19_DROME RL19_RAT RL21_RAT RL22_ICTPU RL23A_RAT RL23_CLOCE RL23_DROME RL24_GILMI RL26_MOUSE RL27A_BOVIN RL27_RAT RL28_LEGPL RL28_MOUSE RL29_YEAST RL30_RAT RL31_PAROL RL32_BOVIN RL34_AEDAL RL35A_XENLA RL35_RAT RL36_IXOSC RL371_DROME RL37A_CRYST RL38_BRABE RL39_SPOFR RL3_HUMAN RL40_DROME RL40_SHEEP RL44Q_CANMA RL4_URECA RL5_STYCL RL6_MOUSE RL7A_TAKRU RL7_PONAB RL8_XENTR RL9_SPOFR RLA0_RANSY RLA2_BRAFL RLMM_KLEP7 RM12_MOUSE RME6_DROME RN151_BOVIN RN19A_HUMAN RN213_MOUSE RNKA_XENLA RNP4_PICTO RNS1_ARATH RO60_HUMAN ROA2_PONAB ROP_DROME RPAB5_MOUSE RPB1_FRG3G RPB1_PLAFD RPB7_RAT RPC10_HUMAN RPC4_HUMAN RPN1_MOUSE RPN2_PONAB RPOA_SPIOL RPOB_DESAH RPOC2_CUCSA RPOC2_VITVI RPOC_LAWIP RRF_NOCSJ RRP36_AJECG RS10_CLOTH RS11_RAT RS12_CHICK RS13_PYRIL RS13_RAT RS14_MOUSE RS15A_DROYA RS15_ORYSJ RS16_DROME RS17_BOVIN RS18_ARGIR RS19_ARGIR RS20_CAMFF RS20_RAT RS21_PECGU RS23_DERVA RS24_ICTPU RS26_OCTVU RS27A_CHICK RS29_IXOSC RS2_HUMAN RS31_XENLA RS3A_APLCA RS3_RAT RS4_IXOSC RS5_HUMAN RS6_APLCA RS7_RAT RS8_RHOBA RS8_SPOFR RSH4A_MOUSE RSMA_CHLCV RSMG_SYNJB RSPH1_MOUSE RSSA_PINFU RT15_DROME RT23_BOVIN RTF1_HUMAN RU17_BOVIN RUVA_HAES2 S10AC_PIG S22A5_HUMAN S23A2_XENTR S2538_MOUSE S27A2_RAT S39AB_XENTR S4A10_MOUSE S4A11_MOUSE S4A4_AMBTI S61A2_MOUSE SAHHA_XENLA SAM5B_DANRE SAP18_BOVIN SAP3_HUMAN SAR1_CAEEL SAS_DROME SBP1_XENTR SBSPO_HUMAN SC16A_HUMAN SC61G_XENLA SC6A1_RAT SC6A6_RAT SC6A9_XENLA SCRB2_RAT SCUB2_MOUSE SDCB1_RAT SEC13_RAT SEC31_USTMA SECA_GLOVI SECE_STAAC SELS_DANRE SEM5A_HUMAN SEPT2_CHICK SEPT4_PONAB SERP2_MOUSE SESN1_XENLA SET5_CANGA SETD2_HUMAN SET_HUMAN SF3B1_MOUSE SFPQ_MOUSE SFSWA_MOUSE SGPL1_RAT SH3G2_MOUSE SLC31_HUMAN SLC31_RAT SLX4_CANGA SLX4_SCLS1 SMRC2_HUMAN SMUF2_XENLA SNAPN_KLULA SO1A1_RAT SO1C1_MOUSE SO4A1_MOUSE SOAT_BOVIN SODC_NICPL SOX14_DANRE SOX4_MOUSE SPAG6_MOUSE SPAG8_HUMAN SPAT6_BOVIN SPCS1_BOVIN SPEB_CHICK SPG21_DANRE SPI2_CRAVI SPO73_YEAST SPTB2_HUMAN SPTCA_DROME SPTN1_CHICK SPX2_DANRE SR140_MOUSE SRP19_DROME SRSF6_HUMAN SSY3_ARATH STA5A_HUMAN STB2_YEAST STC_ONCMY STING_XENTR STPG2_DANRE STRN3_BOVIN STX12_MOUSE SUCB1_MOUSE SUFU_MOUSE SUI1_ANOGA SUIS_RAT SUMT_METJA SVEP1_MOUSE SVIL_BOVIN SYC_RHOBA SYD_DICTD SYEM_CHICK SYE_METBU SYE_MYCMO SYF1_RAT SYFB_CLOTE SYFB_MOUSE SYFB_MYCS5 SYH_MACCJ SYK_MOUSE SYL2_SULSO SYNE1_HUMAN SYPM_RAT SYP_THEVO SYR_TRIEI SYTL5_MOUSE T2FA_DROME TAF11_MOUSE TAMO_DROME TAR1_YEAST TB10B_HUMAN TBA1_CHICK TBA3_DROME TBATA_HUMAN TBB4B_RAT TBB_LYTPI TBB_PARLI TBB_STRPU TBCB_BOVIN TBCD8_MOUSE TBG1_BOVIN TC1D2_MOUSE TCB2_CAEBR TCPB_BOVIN TCPD_MOUSE TCPQ_CHICK TCPZ_RABIT TDRD9_HUMAN TEF_RAT TEKT2_HUMAN TEKT3_BOVIN TEKT3_HUMAN TEKT4_XENLA TENS3_MOUSE TEPP_MOUSE TERA_XENLA TFPI1_RABIT THA11_BOVIN THIC_RHOPB THIE_NOCFA THIG_WOLSU THIK2_ARATH THOC5_CHICK THYG_RAT TICN3_HUMAN TIG_PSESM TIM13_NEUCR TISB_MOUSE TITIN_HUMAN TLL1_XENLA TM10B_DANRE TM145_MOUSE TM233_HUMAN TM258_MOUSE TMA7_DANRE TMCO1_RAT TMEDE_DROAN TMM59_MOUSE TMOD_CAEEL TNR6A_MOUSE TO401_DROME TOM20_XENTR TOM70_HUMAN TOM7_HUMAN TPC11_DANRE TPC6B_HUMAN TPMT_RAT TPPC5_CHICK TPS7_ARATH TPSGC_SOLLC TRA1_SCHPO TRAF3_MOUSE TRCB_XENLA TRI56_BOVIN TRIB2_MOUSE TRIM3_RAT TRIPB_HUMAN TRMB_CAEBR TRMB_UREPA TRN2_DATST TRP4_ARATH TRPA1_HUMAN TRPC5_RABIT TRPD_BURVG TRPD_GEOSL TRPF_PSESM TRY7_ANOGA TSC1_HUMAN TSP1_MOUSE TUT7_HUMAN TYB4_MOUSE TYDC1_PAPSO TYPH_RHOP5 TYR3_CAEEL TYSY_DROME TYY1_HUMAN U2AF2_DROME U520_HUMAN UAF30_SCHPO UB2Q1_MOUSE UBCD6_DROME UBP10_CHICK UBP11_HUMAN UBX_JUNCO UCHL_APLCA UCRI_LAGLA UGAT_BELPE UNC5B_HUMAN UNC79_MOUSE UNC89_CAEEL UTP25_PHANO UVRC_GRABC UXS1_HUMAN VA0E2_HUMAN VAS1_BOVIN VATB2_ACEAT VATB_MANSE VATG3_XENLA VATL_TORMA VAV2_HUMAN VDAC2_XENLA VE6_HPV20 VF71_ASFM2 VIGLN_HUMAN VIPR1_MOUSE VLDLR_RABIT VM31_BOTAT VMP03_EULPE VPS11_HUMAN VPS4B_BOVIN VPS51_DANRE VWDE_MOUSE WAPB_PSEAU WAPL_HUMAN WASL_BOVIN WBP11_RAT WDR16_MOUSE WDR5_BOVIN WDR93_HUMAN WDY_CULQU WNT1_STRPU WNT4_HUMAN WWOX_CHICK XBP1_BOVIN XIAP_MOUSE XPOT_ASPNC XPT_CHLSY XRRA1_MACFA XYLA_ARATH Y0971_DICDI Y1388_SYNY3 Y1677_ARATH Y187_BREBN Y224_HAEIN Y3164_BRUA2 Y5188_ARATH YAP1_HUMAN YBOXH_APLCA YGC1_SCHPO YIPF5_MACFA YL021_MOUSE YL47_SCHPO YNZ9_CAEEL YTHD2_HUMAN YTM1_MAGO7 YUC8_ARATH ZB183_XENLA ZBT14_CHICK ZFHX4_HUMAN ZFP26_MOUSE ZFR_HUMAN ZFY19_MOUSE ZFY26_RAT ZGPAT_DANRE ZN235_MOUSE ZN407_HUMAN ZN501_HUMAN ZN622_MOUSE ZNT1_RAT
*** To show only columns of interest in SQLShare***
SELECT Column1, term, GOSlim_bin, aspect FROM [graceac9@washington.edu].[olur_blastx_uniprot_2d.tab]olur
left join
[sr320@washington.edu].[SPID and GO Numbers]go
on
olur.Column3=go.SPID
left join
[sr320@washington.edu].[GO_to_GOslim]slim
on
go.GOID=slim.GO_id
where aspect like 'P'
!tail ~/Downloads/olur_blastx_uniprot_GOSlim_P.csv
Above is condensed version of /Volumes/web/scaphapoda/Grace/Olur_goslim_a.tab ... condensed to show mainly the category of biological process it is responsible for
!awk '{print $4}' ~/Downloads/olur_blastx_uniprot_GOSlim_P.csv | sort | uniq
4-hydroxy-L-proline,protein A,other ADP-ribosylation,protein ATPase B CoA-linked""",other DNA DNA-dependent""",RNA ERK1 G-protein G2/M GTPase Golgi Gram-positive I I-kappaB JNK JUN MAP MAPK MAPKKK N-linked NADH NF-kappaB NF-kappaB,signal NFAT Notch RNA RNA,other Rab Ras Rho S TOR UV,other V(D)J Wnt a abscisic acid actin activated active activity,cell-cell activity,other activity,protein activity,signal adhesion adhesion,cell after agglutination,stress aggregate aldosterone alkaline amino and angiogenesis,developmental antimicrobial apical assembly,cell assembly,developmental autophagic autophosphorylation,protein axonogenesis,cell axonogenesis,developmental bacterium,stress balance,other base beta biogenesis,other biological biosynthetic blood bone branching by c cGMP calcium calcium-mediated camera-type capping,cell capping,protein cardiac caspase catabolic catalytic catecholamine cell cell-matrix cell-substrate cellular center central chain,other checkpoint,cell cholesterol chondroitin class clearance,cell coagulation,other cocaine,other collagen collateral complex contact,other containing contraction,other cortical coupled cyclase cycle cycle,cell cyclic cyclin-dependent cyst cytokine-mediated cytoskeleton damage defense dendrite dephosphorylation,protein depolymerization,cell deprivation,stress derivative detection determination,developmental determination,other development,cell development,developmental development,other diameter,other differentiation,developmental differentiation,other dipeptide,other disc-derived distribution,cell division,other dopamine dsRNA,other electron embryonic endocytosis,cell endonucleolytic""",DNA endopeptidase endothelial epidermal epithelial epithelium,developmental erythrocyte estrogen ethanol,other expression,other extracellular factor family fat female fiber fibroblast fidelity,protein filament filopodium foam focal folding follicle,developmental foreign formation formation,cell formation,developmental forming from fungus,stress gametogenesis,DNA gamma-aminobutyric gamma-delta gene genitalia glial glucose glycosylation,protein growth growth,other heart heat,stress heterochronic""",other hh histone homeostasis,other hormone host hydrolase hypusine,protein identity, imaginal immune immunoglobulin in inflammatory initiation,protein injury,stress innate insulin integrity, interaction interferon-beta interferon-gamma interleukin-10 interleukin-2 internalization,cell internalization,protein intestinal into intracellular involved ion ion,other island,DNA killer kinase lamellocyte levels,cell-cell levels,other life ligase light linked lipid localization,other location locomotion,other lymphocyte mRNA macrophage maintenance,other male mammary mast mediated meiosis,cell membrane metabolic metabolites metaphase/anaphase miRNA, microtubule migration,developmental migration,other mineralization,developmental mitochondrial mitochondrion,cell mitotic modification,RNA monomers,cell monomers,protein morphogenesis,developmental motility,other movement,other multicellular muscle myeloid myoblast natural necrosis neuromuscular neuron neurotransmitter nitric nitrogen,other nuclear nucleotide nucleus, nucleus,other of open organism organisms,other organization organization,cell organization,cell-cell ossification,developmental osteoblast osteoclast oxidative oxygen pH,other pain,other pain,stress pathway pathway""",protein pathway""",stress pathway,protein pathway,signal pathway,stress pattern patterning,developmental peptidase peptidyl-serine peptidyl-threonine peptidyl-tyrosine permeability,other peroxide,stress peroxisome phagocytosis, phagocytosis,cell phosphatase phosphate phosphoinositide phosphorylation,other phosphorylation,protein phosphorylation,signal pinocytosis,cell plasm plasma plasticity,cell-cell platelet,cell-cell platelet,stress platelet-derived point polarity,cell polarity,developmental polarization,cell polarization,developmental polarized polymerase potassium potential potential,other pre-catalytic presentation presentation,other pressure,other process""",other process, process,other process,protein process,stress processing,RNA production,other projection proliferation proliferation,cell proteasomal protein protein,stress proteolysis,protein proton pupal radiation,other reactive receptivity,other receptor receptor-mediated remodeling,cell repeat replication,DNA replication,cell respiration,other response response,other secreting secretion,cell-cell segregation,cell selection,RNA selection,cell selection,developmental sequestering shape,cell signal signaling signaling,signal sister size, skeletal sleep/wake smell,other smooth smoothened sodium sound,other specification,cell specification,developmental spindle splicing, splicing,RNA stability,RNA stability,protein starvation,stress stereocilium steroid stimulus stimulus,other storage,other stress stress,stress structural substance,other survival symmetry,developmental synaptic system system,signal targeting taste,other telomerase telomere terminal termination,cell termination,protein tissue to tooth tooth,developmental tracheal transcription transcription, transduction,signal transforming transition transition,cell transition,developmental translation translation,protein translational translocation,signal transmission,cell-cell transport triglyceride tumor tyrosine ubiquinol ubiquitin-dependent ubiquitin-protein ubiquitination,protein unwinding,RNA ureteric using vascular vasoconstriction,other vesicle vesicle-mediated vessel vessels,developmental via virus,stress with within
A lot of unique categories. Now to attempt to sort into broader genres for pie chart
!fgrep --color "mammary" ~/Downloads/olur_blastx_uniprot_GOSlim_P.csv
Why is there "mammary"...?
!fgrep --color "growth" ~/Downloads/olur_blastx_uniprot_GOSlim_P.csv
"growth" and "cell" too broad...
!fgrep --color "cell" ~/Downloads/olur_blastx_uniprot_GOSlim_P.csv
!fgrep --color "developmental" ~/Downloads/olur_blastx_uniprot_GOSlim_P.csv
"developmental" too broad...
!fgrep --color "genitalia" ~/Downloads/olur_blastx_uniprot_GOSlim_P.csv
!fgrep --color "hermaphrodite" ~/Downloads/olur_blastx_uniprot_GOSlim_P.csv
!fgrep --color "gonad" ~/Downloads/olur_blastx_uniprot_GOSlim_P.csv
!fgrep --color "sex" ~/Downloads/olur_blastx_uniprot_GOSlim_P.csv
!fgrep --color "female" ~/Downloads/olur_blastx_uniprot_GOSlim_P.csv
!fgrep --color "pregnancy" ~/Downloads/olur_blastx_uniprot_GOSlim_P.csv
!fgrep --color "male" ~/Downloads/olur_blastx_uniprot_GOSlim_P.csv
!fgrep --color "meiosis" ~/Downloads/olur_blastx_uniprot_GOSlim_P.csv
!fgrep --color "gonad development" ~/Downloads/olur_blastx_uniprot_GOSlim_P.csv
!fgrep --color "germarium" ~/Downloads/olur_blastx_uniprot_GOSlim_P.csv
!fgrep --color "oocyte" ~/Downloads/olur_blastx_uniprot_GOSlim_P.csv
!fgrep --color "ovarian" ~/Downloads/olur_blastx_uniprot_GOSlim_P.csv
!fgrep --color "sex determination" ~/Downloads/olur_blastx_uniprot_GOSlim_P.csv
!fgrep --color "germ-line" ~/Downloads/olur_blastx_uniprot_GOSlim_P.csv
!fgrep --color "reproduction" ~/Downloads/olur_blastx_uniprot_GOSlim_P.csv
"viral reproduction"...? what?
!fgrep --color "estrogen" ~/Downloads/olur_blastx_uniprot_GOSlim_P.csv
!fgrep --color "testosterone" ~/Downloads/olur_blastx_uniprot_GOSlim_P.csv
!fgrep --color "androgen" ~/Downloads/olur_blastx_uniprot_GOSlim_P.csv
!fgrep --color "stem cell" ~/Downloads/olur_blastx_uniprot_GOSlim_P.csv
"stem cell" just refers to an undifferentiated cell... nothing to really do with reproduction
!fgrep --color "mating" ~/Downloads/olur_blastx_uniprot_GOSlim_P.csv
!egrep -wi --color 'mating | stem cell | androgen' /Volumes/web/scaphapoda/Grace/Blasts/olur_blastx_uniprot_GOSlim_P.csv
!fgrep --color "mating" /Volumes/web/scaphapoda/Grace/Blasts/olur_blastx_uniprot_GOSlim_P.csv
!fgrep --color "embryonic" ~/Downloads/olur_blastx_uniprot_GOSlim_P.csv
Is "embryonic" useful...?
!fgrep --color "genitalia, hermaphrodite, gonad, sex, female, pregnancy, male, gonad development, germarium, oocyte, ovarian, sex-determination, germ-line, reproduction, estrogen, testosterone, androgen, stem cell, mating, embryonic" ~/Downloads/olur_blastx_uniprot_GOSlim_P.csv
What if there are overlap between the categories? i.e. a protein falls under more than one of the "fgrep"s...?
!tr ',' "\t" <~/Downloads/olur_blastx_uniprot_GOSlim_P.csv> ~/Downloads/olur_blastx_uniprot_GOSlim_P.tab
!head ~/Downloads/olur_blastx_uniprot_GOSlim_P.tab
Changed the "," in the syntax to tabs so that the data could be better seen in columns
!python ~/Downloads/olur_blastx_uniprot_GOSlim_P.tab -f tsv -o justslim.txt
File "/Users/srlab/Downloads/olur_blastx_uniprot_GOSlim_P.tab", line 1 Column1 term GOSlim_bin aspect ^ SyntaxError: invalid syntax
still doesnt like the syntax
Maybe the word "term" is the problem... new GOSlim_bin file without the word "term"
Nope. Steven Showed me how to do it below
!tr ',' "\t" </Volumes/web/scaphapoda/Grace/olur_blastx_uniprot_GOSlimP-noterm.csv> /Volumes/web/scaphapoda/Grace/olur_blastx_uniprot_GOSlimP-noterm.tab
!head /Volumes/web/scaphapoda/Grace/olur_blastx_uniprot_GOSlimP-noterm.tab
*Have to type "pylab inline" if want to make graphs within iPython*
pylab inline
Populating the interactive namespace from numpy and matplotlib
WARNING: pylab import has clobbered these variables: ['load', 'info', 'save', 'datetime', 'unique'] `%matplotlib` prevents importing * from pylab and numpy
from pandas import *
jslim = read_table("/Volumes/web/scaphapoda/Grace/olur_blastx_uniprot_GOSlimP-noterm.tab", # name of the data file
#sep=",", # what character separates each column?
na_values=["", " "]) # what values should be considered "blank" values?
jslim.head
<bound method DataFrame.head of Column1 GOSlim_bin aspect 0 Ostrea_lur_contig1 protein metabolism P 1 Ostrea_lur_contig10 protein metabolism P 2 Ostrea_lur_contig100 RNA metabolism P 3 Ostrea_lur_contig100 RNA metabolism P 4 Ostrea_lur_contig100 RNA metabolism P 5 Ostrea_lur_contig100 RNA metabolism P 6 Ostrea_lur_contig100 RNA metabolism P 7 Ostrea_lur_contig100 RNA metabolism P 8 Ostrea_lur_contig1001 other metabolic processes P 9 Ostrea_lur_contig1001 other metabolic processes P 10 Ostrea_lur_contig1001 other metabolic processes P 11 Ostrea_lur_contig1001 other metabolic processes P 12 Ostrea_lur_contig1004 other biological processes P 13 Ostrea_lur_contig1004 signal transduction P 14 Ostrea_lur_contig1004 signal transduction P 15 Ostrea_lur_contig1004 other biological processes P 16 Ostrea_lur_contig1005 other metabolic processes P 17 Ostrea_lur_contig1005 other metabolic processes P 18 Ostrea_lur_contig1005 other metabolic processes P 19 Ostrea_lur_contig1005 other metabolic processes P 20 Ostrea_lur_contig1005 other metabolic processes P 21 Ostrea_lur_contig1005 other metabolic processes P 22 Ostrea_lur_contig1005 other metabolic processes P 23 Ostrea_lur_contig1005 other metabolic processes P 24 Ostrea_lur_contig1005 other metabolic processes P 25 Ostrea_lur_contig1007 RNA metabolism P 26 Ostrea_lur_contig1007 RNA metabolism P 27 Ostrea_lur_contig1008 RNA metabolism P 28 Ostrea_lur_contig1008 RNA metabolism P 29 Ostrea_lur_contig1008 RNA metabolism P 30 Ostrea_lur_contig1008 cell organization and biogenesis P 31 Ostrea_lur_contig1008 RNA metabolism P 32 Ostrea_lur_contig1008 cell organization and biogenesis P 33 Ostrea_lur_contig1008 RNA metabolism P 34 Ostrea_lur_contig1008 transport P 35 Ostrea_lur_contig1008 RNA metabolism P 36 Ostrea_lur_contig1008 other metabolic processes P 37 Ostrea_lur_contig1008 RNA metabolism P 38 Ostrea_lur_contig1008 RNA metabolism P 39 Ostrea_lur_contig1009 other biological processes P 40 Ostrea_lur_contig1009 other metabolic processes P 41 Ostrea_lur_contig1009 other biological processes P 42 Ostrea_lur_contig101 other metabolic processes P 43 Ostrea_lur_contig101 other metabolic processes P 44 Ostrea_lur_contig101 other metabolic processes P 45 Ostrea_lur_contig101 other metabolic processes P 46 Ostrea_lur_contig101 other metabolic processes P 47 Ostrea_lur_contig101 other metabolic processes P 48 Ostrea_lur_contig1010 death P 49 Ostrea_lur_contig1010 death P 50 Ostrea_lur_contig1010 stress response P 51 Ostrea_lur_contig1010 death P 52 Ostrea_lur_contig1010 death P 53 Ostrea_lur_contig1011 other metabolic processes P 54 Ostrea_lur_contig1011 stress response P 55 Ostrea_lur_contig1012 transport P 56 Ostrea_lur_contig1012 protein metabolism P 57 Ostrea_lur_contig1012 cell organization and biogenesis P 58 Ostrea_lur_contig1012 transport P 59 Ostrea_lur_contig1012 cell organization and biogenesis P ... ... ... [5906 rows x 3 columns]>
!fgrep -c "DNA metabolism" /Volumes/web/scaphapoda/Grace/olur_blastx_uniprot_GOSlimP-noterm.tab
92
!fgrep -c "RNA metabolism" /Volumes/web/scaphapoda/Grace/olur_blastx_uniprot_GOSlimP-noterm.tab
551
!fgrep -c "cell adhesion" /Volumes/web/scaphapoda/Grace/olur_blastx_uniprot_GOSlimP-noterm.tab
73
!fgrep -c "cell cycle and proliferation" /Volumes/web/scaphapoda/Grace/olur_blastx_uniprot_GOSlimP-noterm.tab
214
!fgrep -c "cell organization and biogenesis" /Volumes/web/scaphapoda/Grace/olur_blastx_uniprot_GOSlimP-noterm.tab
465
!fgrep -c "cell-cell signaling" /Volumes/web/scaphapoda/Grace/olur_blastx_uniprot_GOSlimP-noterm.tab
44
!fgrep -c "death" /Volumes/web/scaphapoda/Grace/olur_blastx_uniprot_GOSlimP-noterm.tab
144
!fgrep -c "developmental processes" /Volumes/web/scaphapoda/Grace/olur_blastx_uniprot_GOSlimP-noterm.tab
624
!fgrep --color "developmental processes" ~/Downloads/olur_blastx_uniprot_GOSlim_P.csv
Use the GOSlim file where the aspect of developmental process is listed so that can isolate the ones to do with reproduction/ sex determination/ gonad development/ etc.
!fgrep -c "other biological processes" /Volumes/web/scaphapoda/Grace/olur_blastx_uniprot_GOSlimP-noterm.tab
886
!fgrep -c "other metabolic processes" /Volumes/web/scaphapoda/Grace/olur_blastx_uniprot_GOSlimP-noterm.tab
1034
!fgrep -c "protein metabolism" /Volumes/web/scaphapoda/Grace/olur_blastx_uniprot_GOSlimP-noterm.tab
527
!fgrep -c "signal transduction" /Volumes/web/scaphapoda/Grace/olur_blastx_uniprot_GOSlimP-noterm.tab
303
!fgrep -c "stress response" /Volumes/web/scaphapoda/Grace/olur_blastx_uniprot_GOSlimP-noterm.tab
266
!fgrep -c "transport" /Volumes/web/scaphapoda/Grace/olur_blastx_uniprot_GOSlimP-noterm.tab
683
!PWD
/Users/srlab
jslim.groupby('GOSlim_bin').Column1.count().plot(kind='bar')
<matplotlib.axes.AxesSubplot at 0x10722b5d0>
Graph looks good, but I don't see a category on reproduction or gonad development
from pylab import *
# make a square figure and axes
figure(1, figsize=(12,12))
ax = axes([0.1, 0.1, 0.8, 0.8])
# The slices will be ordered and plotted counter-clockwise.
labels = 'DNA metabolism', 'RNA metabolism', 'cell adhesion', 'cell cycle and proliferation', 'cell organization and biogenesis', 'cell-cell signaling', 'death', 'developmental processes', 'other biological processes', 'other metabolic processes', 'protein metabolism', 'signal transduction', 'stress response', 'transport'
fracs = [92, 551, 73, 214, 465, 44, 144, 624, 886, 1034, 527, 303, 266, 683]
explode=(0, 0, 0, 0)
pie(fracs, explode=explode, labels=labels,
autopct='%1.1f%%', shadow=True, startangle=0)
# The default startangle is 0, which would start
# the Frogs slice on the x-axis. With startangle=90,
# everything is rotated counter-clockwise by 90 degrees,
# so the plotting starts on the positive y-axis.
title('Biological processes', bbox={'facecolor':'0.8', 'pad':5})
show()
--------------------------------------------------------------------------- AssertionError Traceback (most recent call last) <ipython-input-18-30a35a313238> in <module>() 11 12 pie(fracs, explode=explode, labels=labels, ---> 13 autopct='%1.1f%%', shadow=True, startangle=0) 14 # The default startangle is 0, which would start 15 # the Frogs slice on the x-axis. With startangle=90, /usr/local/bioinformatics/anaconda/lib/python2.7/site-packages/matplotlib/pyplot.pyc in pie(x, explode, labels, colors, autopct, pctdistance, shadow, labeldistance, startangle, radius, hold) 2967 autopct=autopct, pctdistance=pctdistance, shadow=shadow, 2968 labeldistance=labeldistance, startangle=startangle, -> 2969 radius=radius) 2970 draw_if_interactive() 2971 finally: /usr/local/bioinformatics/anaconda/lib/python2.7/site-packages/matplotlib/axes.pyc in pie(self, x, explode, labels, colors, autopct, pctdistance, shadow, labeldistance, startangle, radius) 5400 explode = [0] * len(x) 5401 assert(len(x) == len(labels)) -> 5402 assert(len(x) == len(explode)) 5403 if colors is None: 5404 colors = ('b', 'g', 'r', 'c', 'm', 'y', 'k', 'w') AssertionError:
# Don't understand what AssertionError is saying or how to fix it.
Below could be how to do it...
df = DataFrame('/Volumes/web/scaphapoda/Grace/olur_blastx_uniprot_GOSlimP-noterm.tab', index=['DNA metabolism', 'RNA metabolism', 'cell adhesion', 'cell cycle and proliferation', 'cell organization and biogenesis', 'cell-cell signaling', 'death', 'developmental processes', 'other biological processes', 'other metabolic processes', 'protein metabolism', 'signal transduction', 'stress response', 'transport'], columns=['GOSlim_bin'])
df.plot(kind='pie', subplots=True)
--------------------------------------------------------------------------- NameError Traceback (most recent call last) <ipython-input-20-88d5617154a1> in <module>() ----> 1 df = DataFrame('/Volumes/web/scaphapoda/Grace/olur_blastx_uniprot_GOSlimP-noterm.tab', index=['DNA metabolism', 'RNA metabolism', 'cell adhesion', 'cell cycle and proliferation', 'cell organization and biogenesis', 'cell-cell signaling', 'death', 'developmental processes', 'other biological processes', 'other metabolic processes', 'protein metabolism', 'signal transduction', 'stress response', 'transport'], columns=['GOSlim_bin']) 2 df.plot(kind='pie', subplots=True) NameError: name 'DataFrame' is not defined
#I don't really know what the DataFrame aspect means or why it's saying "invalid chart type given pie"
#Also, where do I put the link to the data in the above code? is that instead of the (3 * rand(14,1)...?)